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choderalab / espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
https://docs.espaloma.org/en/latest/
MIT License
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Called setPositions() on a Context with the wrong number of positions #194

Open hanboy315 opened 1 year ago

hanboy315 commented 1 year ago

Trying to use the pre-trained espaloma-0.3.0 on my supercell, and came across this vague error that I can't seem to get the origin of?

/home/hy2120/miniconda/envs/openff/lib/python3.10/site-packages/dgl/heterograph.py:72: DGLWarning: Recommend creating graphs by `dgl.graph(data)` instead of `dgl.DGLGraph(data)`.
  dgl_warning('Recommend creating graphs by `dgl.graph(data)'
/home/hy2120/miniconda/envs/openff/lib/python3.10/site-packages/dgl/backend/pytorch/tensor.py:352: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
  assert input.numel() == input.storage().size(), "Cannot convert view " \
Traceback (most recent call last):
  File "<stdin>", line 25, in <module>
  File "/home/hy2120/miniconda/envs/openff/lib/python3.10/site-packages/openmm/openmm.py", line 3479, in setPositions
    return _openmm.Context_setPositions(self, positions)
openmm.OpenMMException: Called setPositions() on a Context with the wrong number of positions
mikemhenry commented 1 year ago

@hanboy315 I edited your post to make it more clear.

Thank you for the bug report! Can you share the script you used that produced this error? What is the output of conda list for your environment?

hanboy315 commented 1 year ago

thanks! 

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
ambertools                23.3            py310he275f01_2    conda-forge
amberutils                21.0                     pypi_0    pypi
annotated-types           0.5.0              pyhd8ed1ab_0    conda-forge
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
arrow                     1.2.3              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
aws-c-auth                0.7.3                he2921ad_3    conda-forge
aws-c-cal                 0.6.2                hc309b26_0    conda-forge
aws-c-common              0.9.0                hd590300_0    conda-forge
aws-c-compression         0.2.17               h4d4d85c_2    conda-forge
aws-c-event-stream        0.3.2                h2e3709c_0    conda-forge
aws-c-http                0.7.12               hc865f51_1    conda-forge
aws-c-io                  0.13.32              h019f825_2    conda-forge
aws-c-mqtt                0.9.5                h3a0376c_1    conda-forge
aws-c-s3                  0.3.14               h1678ad6_3    conda-forge
aws-c-sdkutils            0.1.12               h4d4d85c_1    conda-forge
aws-checksums             0.1.17               h4d4d85c_1    conda-forge
aws-crt-cpp               0.23.1               h40cdbb9_0    conda-forge
aws-sdk-cpp               1.11.156             h8bde0db_1    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
boost                     1.78.0          py310hc4a4660_4    conda-forge
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
brotli                    1.1.0                hd590300_0    conda-forge
brotli-bin                1.1.0                hd590300_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_0    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.19.1               hd590300_0    conda-forge
c-blosc2                  2.10.2               hb4ffafa_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.1              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h0c91306_1017    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.0           py310hd41b1e2_0    conda-forge
cudatoolkit               11.8.0              h4ba93d1_12    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
debugpy                   1.7.0           py310hc6cd4ac_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dgl                       0.9.1post1              py310_0    dglteam
edgembar                  0.2                      pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
espaloma                  0.3.1              pyhd8ed1ab_1    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fftw                      3.3.10          nompi_hc118613_108    conda-forge
filelock                  3.12.3             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.42.1          py310h2372a71_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
glog                      0.6.0                h6f12383_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2           py310h3ec546c_1    conda-forge
greenlet                  2.0.2           py310hc6cd4ac_1    conda-forge
h5py                      3.9.0           nompi_py310hcca72df_101    conda-forge
hdf4                      4.2.15               h501b40f_6    conda-forge
hdf5                      1.14.1          nompi_h4f84152_100    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.0.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.25.2             pyh2140261_0    conda-forge
ipython                   8.15.0             pyh0d859eb_0    conda-forge
ipywidgets                8.1.0              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.0             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
jsonschema                4.19.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.0             pyhd8ed1ab_1    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.1           py310hff52083_0    conda-forge
jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge
jupyter_server            2.7.3              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.5              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.24.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.8              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py310hd41b1e2_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.38                 h1181459_1  
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20230125.3      cxx17_h59595ed_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libarrow                  13.0.0           h1ed0495_3_cpu    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_0    conda-forge
libbrotlidec              1.1.0                hd590300_0    conda-forge
libbrotlienc              1.1.0                hd590300_0    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   8.2.1                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libglib                   2.76.4               hebfc3b9_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libgoogle-cloud           2.12.0               h840a212_1    conda-forge
libgrpc                   1.56.2               h3905398_1    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_he09a3a9_107    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libnuma                   2.0.16               h0b41bf4_1    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libprotobuf               4.23.3               hd1fb520_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libthrift                 0.19.0               h8fd135c_0    conda-forge
libtiff                   4.5.1                h8b53f26_1    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.46.0               hd590300_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzip                    1.10.1               h2629f0a_2    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lxml                      4.9.3           py310h9b7343a_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.3           py310h2372a71_0    conda-forge
matplotlib-base           3.7.1           py310he60537e_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.9           py310h8e08b51_0    conda-forge
mistune                   3.0.1              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mpc                       1.3.1                hfe3b2da_0    conda-forge
mpfr                      4.2.0                hb012696_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.5           py310hdf3cbec_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.8.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_hec59055_101    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nglview                   3.0.6              pyhba93850_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  7.0.3              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.4           py310hd91493a_101    conda-forge
numpy                     1.25.2          py310ha4c1d20_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-forcefields        2023.08.0          pyh1a96a4e_0    conda-forge
openff-interchange        0.3.14             pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.3.14             pyhd8ed1ab_0    conda-forge
openff-models             0.1.0              pyh1a96a4e_1    conda-forge
openff-toolkit            0.14.3             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.14.3             pyhd8ed1ab_0    conda-forge
openff-units              0.2.1              pyh1a96a4e_0    conda-forge
openff-utilities          0.1.9              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openmm                    8.0.0           py310h5728c26_1    conda-forge
openmmforcefields         0.11.2             pyhd8ed1ab_1    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
orc                       1.9.0                h385abfd_1    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
pandas                    2.1.0           py310hcc13569_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.7.2              pyhd8ed1ab_0    conda-forge
parmed                    4.1.0           py310heca2aa9_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          4_hd590300_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.0          py310h582fbeb_0    conda-forge
pint                      0.21               pyhd8ed1ab_0    conda-forge
pip                       23.2.1          py310h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.10.0             pyhd8ed1ab_0    conda-forge
plotly                    5.16.1             pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py310h1fa729e_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pyarrow                   13.0.0          py310hf9e7431_3_cpu    conda-forge
pycairo                   1.24.0          py310hda9f760_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.12         py310h2372a71_1    conda-forge
pydantic-core             2.6.3           py310hcb5633a_0    conda-forge
pyedr                     0.7.2              pyhd8ed1ab_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0           py310ha028ce3_2    conda-forge
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytorch                   2.0.0           cpu_generic_py310ha25dcb8_1    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_0    conda-forge
pyzmq                     25.1.1          py310h5bbb5d0_0    conda-forge
qcelemental               0.26.0             pyhd8ed1ab_0    conda-forge
qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge
rdkit                     2023.03.3       py310h399bcf7_0    conda-forge
rdma-core                 28.9                 h59595ed_1    conda-forge
re2                       2023.03.02           h8c504da_0    conda-forge
readline                  8.2                  h5eee18b_0  
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
reportlab                 4.0.4           py310h2372a71_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rlpycairo                 0.2.0              pyhd8ed1ab_0    conda-forge
rpds-py                   0.10.2          py310hcb5633a_0    conda-forge
s2n                       1.3.49               h06160fa_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.11.2          py310ha4c1d20_0    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                68.0.0          py310h06a4308_0  
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleef                     3.5.1                h9b69904_2    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlalchemy                2.0.20          py310h2372a71_0    conda-forge
sqlite                    3.41.2               h5eee18b_0  
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tinydb                    4.8.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h1ccaba5_0  
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3           py310h2372a71_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.7.1                hd8ed1ab_0    conda-forge
typing_extensions         4.7.1              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h04d1e81_0  
ucx                       1.14.1               h64cca9d_4    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.0.4              pyhd8ed1ab_0    conda-forge
validators                0.22.0             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
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wheel                     0.38.4          py310h06a4308_0  
widgetsnbextension        4.0.8              pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
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xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.4.2                h5eee18b_0  
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.16.2             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zlib-ng                   2.0.7                h0b41bf4_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge
hanboy315 commented 1 year ago 

# Run the Python script
# using pretrained espaloma-0.3.0 to generate openmm_system
# https://github.com/choderalab/espaloma

python <<EOF
import os
import torch
import espaloma as esp

from openff.toolkit.utils import get_data_file_path
from openff.toolkit.topology import Molecule
from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout

mol_filepath = get_data_file_path('/home/hy2120/y6/anneal3_2.mol')
molecule = Molecule(mol_filepath)
molecule_graph = esp.Graph(molecule)

espaloma_model = esp.get_model("latest")
espaloma_model(molecule_graph.heterograph)
system = esp.graphs.deploy.openmm_system_from_graph(molecule_graph)

pdb = PDBFile('/home/hy2120/y6/anneal3_2_justified.pdb')

integrator = LangevinMiddleIntegrator(300 * kelvin, 1 / picosecond, 0.004 * picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('/home/hy2120/y6/output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
        potentialEnergy=True, temperature=True))
simulation.step(10000)

EOF
ijpulidos commented 1 year ago

@hanboy315 The error is because you are trying to create a Simulation object from the topology and the system but the system only has the small molecule (from the mol file), whereas the topology is presumably the receptor (from the pdb file). Therefore these two are incompatible (they are not referring to the same systems). For a way to create an unified topology and system with both the receptor and the molecule you can check this example from the openff tutorials.

hanboy315 commented 1 year ago

Hello! Many thanks for the reply. I'm trying to build a box of small molecules only. So I've allowed the topology to be the same as my 'molecule'. If there is only one molecule it works (sure) but if it's >1 the problem remains. My .py now looks something like this. My workflow begins with packmol'ing two small molecules and that is the Y6_2_out.mol/.gro

import os
import torch
import espaloma as esp

from openff.toolkit.utils import get_data_file_path

from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout

from openff.toolkit.topology import Topology, Molecule

from openff.toolkit.utils.toolkits import RDKitToolkitWrapper

# read in molecules to molecular dynamics
startpositions = GromacsGroFile('/home/hy2120/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.gro').positions
mol_filepath = get_data_file_path('/home/hy2120/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.mol') 

# See here: https://docs.openforcefield.org/projects/toolkit/en/stable/users/molecule_cookbook.html#from-small-molecule-pdb-file
molecule = Molecule.from_file(mol_filepath,"mol", toolkit_registry=RDKitToolkitWrapper())
molecule_graph = esp.Graph(molecule)

# load Espaloma
espaloma_model = esp.get_model("latest")
espaloma_model(molecule_graph.heterograph)
omm_system = esp.graphs.deploy.openmm_system_from_graph(molecule_graph)
# OK; we have our force-field now

# ensure we have correct Topology objects (OpenFF and OpenMM, jeese)
off_topology = Topology.from_molecules(molecule)
omm_topology = off_topology.to_openmm()

# Molecular dynamics setup
integrator = LangevinMiddleIntegrator(300 * kelvin, 1 / picosecond, 0.001 * picoseconds)
simulation = Simulation(omm_topology, omm_system, integrator)
simulation.context.setPositions(startpositions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('/home/hy2120/y6/output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
        potentialEnergy=True, temperature=True))
simulation.step(10000)
hanboy315 commented 1 year ago

and the error remained to be 

openmm.OpenMMException: Called setPositions() on a Context with the wrong number of positions
mikemhenry commented 1 year ago

This is a good question, but looks like it belongs in the espaloma repository and not perses since it doesn't look like your script uses perses?

mikemhenry commented 1 year ago

I'll re-open this and transfer it since it has more info (more like the context of our conversation) then the new one you opened @hanboy315

mikemhenry commented 1 year ago

@ijpulidos @yuanqing-wang any ideas here?

jarvist commented 12 months ago

We worked around this by borrowing approaches in #192 and using the EspalomaTemplateGeneratorwhich we then put in an openff.Forcefield object in order to use the openmm.app.Modeller. This approach seemed to be happily start a multi-molecule input file in Espaloma, and though I have not checked carefully the Forcefield is correct, the dynamics looked sensible. I'm always a bit lost debugging Python and end up trying different instantiated objects until something works.

https://github.com/Frost-group/ConjugatedEspaloma/commit/61e52802f27e286931fe2f099d25011e82a8ee0b

mikemhenry commented 11 months ago

@ijpulidos we should update our docs to include a little example like this